|
| Status |
Public on Jun 01, 2017 |
| Title |
EHCont_RNAseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
sorted ETP
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD4-CD8-Lin-CD44+CD25-ckit+
genotype: Wild type
tissue: fetal thymus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted and total RNA was isolated from them using the RNeasy-Micro Kit (Qiagen). The total RNA was then processed for deep sequencing using SMARTer Ultra Low Input RNA kit for Sequencing-v3 (Clontech) following the manufacturer’s protocol.
Liibraies were prepared fromt the sonicated DNA using Low Input Library Prep Kit (Clontech) following the manufacturer’s protocol. cDNA libraries were sequenced with a HiSeq 2500 sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CD4–CD8–Lin–CD44+CD25–ckit+
|
| Data processing |
Illumina bcl2fastq-1.8.4 software used for basecalling.
Paired-end RNA-Seq reads were trimmed before mapping using fastx-trimmer tool.
TopHat (version 2.0.14) was used to map reads to the mouse reference genome (mm9)
Array Studio software (OmicSoft Corporation) was used to calculate raw read counts.
Abundance values (counts) were normalized and compared between control vs double KO mice using DESeq (version 2) .
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include the abundance values of control (3 samples) and dKO (3samples) with P-value generated by DESeq (version 2) .
|
| |
|
| Submission date |
Feb 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuko Miyazaki |
| E-mail(s) |
kamiyazaki@infront.kyoto-u.ac.jp
|
| Organization name |
Institute for Life and Medical Sciences, Kyoto University
|
| Lab |
Department of Immunology
|
| Street address |
53 Kawahara-cho, Shogoin, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE95337 |
Innate versus adaptive lymphoid cell fate choice is controlled by the E-Id protein axis [RNA-Seq] |
| GSE95339 |
Innate versus adaptive lymphoid cell fate choice is controlled by the E-Id protein axis |
|
| Relations |
| BioSample |
SAMN06445825 |
| SRA |
SRX2586526 |
